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root/OpenMD/trunk/src/applications/staticProps/StaticPropsCmd.cpp

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (file contents), Revision 544 by tim, Fri May 27 04:41:34 2005 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (file contents), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	File autogenerated by gengetopt version 2.11
2	>	File autogenerated by gengetopt version 2.22.4
3		generated with the following command:
4	<	/home/maul/gezelter/tim/bin/gengetopt -i StaticProps.ggo -F StaticPropsCmd
4	>	gengetopt -i StaticProps.ggo -c cpp -F StaticPropsCmd -u
5
6		The developers of gengetopt consider the fixed text that goes in all
7		gengetopt output files to be in the public domain:
8		we make no copyright claims on it.
9		*/
10
11	+	/* If we use autoconf.  */
12	+	#ifdef HAVE_CONFIG_H
13	+	#include "config.h"
14	+	#endif
15
16		#include <stdio.h>
17		#include <stdlib.h>
18		#include <string.h>
19
20	<	/* If we use autoconf.  */
21	<	#ifdef HAVE_CONFIG_H
18	<	#include "config.h"
20	>	#ifndef FIX_UNUSED
21	>	#define FIX_UNUSED(X) (void) (X) /* avoid warnings for unused params */
22		#endif
23
24	<	#include "getopt.h"
24	>	#ifdef WIN32
25	>	#include "utils/wingetopt.h"
26	>	#else
27	>	#include <getopt.h>
28	>	#endif
29
30		#include "StaticPropsCmd.h"
31
32	<	void
26	<	cmdline_parser_print_version (void)
27	<	{
28	<	printf ("%s %s\n", CMDLINE_PARSER_PACKAGE, CMDLINE_PARSER_VERSION);
29	<	}
32	>	const char *gengetopt_args_info_purpose = "";
33
34	<	void
32	<	cmdline_parser_print_help (void)
33	<	{
34	<	cmdline_parser_print_version ();
35	<	printf("\n"
36	<	"Usage: %s [OPTIONS]...\n", CMDLINE_PARSER_PACKAGE);
37	<	printf("\n");
38	<	printf("  -h, --help                      Print help and exit\n");
39	<	printf("  -V, --version                   Print version and exit\n");
40	<	printf("  -i, --input=filename            input dump file\n");
41	<	printf("  -o, --output=filename           output file name\n");
42	<	printf("  -n, --step=INT                  process every n frame  (default=`1')\n");
43	<	printf("  -r, --nrbins=INT                number of bins for distance  (default=`100')\n");
44	<	printf("  -a, --nanglebins=INT            number of bins for cos(angle)  (default=\n                                    `50')\n");
45	<	printf("  -l, --length=DOUBLE             maximum length (Defaults to 1/2 smallest \n                                    length of first frame)\n");
46	<	printf("      --sele1=selection script    select the first stuntdouble set\n");
47	<	printf("      --sele2=selection script    select the second stuntdouble set\n");
48	<	printf("      --sele3=selection script    select the third stuntdouble set\n");
49	<	printf("      --refsele=selection script  select reference (use and only use with \n                                    --gxyz)\n");
50	<	printf("      --molname=STRING            molecule name\n");
51	<	printf("      --begin=INT                 begin interanl index\n");
52	<	printf("      --end=INT                   end internal index\n");
53	<	printf("\n");
54	<	printf(" Group: staticProps  an option of this group is required\n");
55	<	printf("      --gofr                      g(r)\n");
56	<	printf("      --r_theta                   g(r, cos(theta))\n");
57	<	printf("      --r_omega                   g(r, cos(omega))\n");
58	<	printf("      --theta_omega               g(cos(theta), cos(omega))\n");
59	<	printf("      --gxyz                      g(x, y, z)\n");
60	<	printf("      --p2                        p2 order parameter (--sele1 and --sele2 must \n                                    be specified)\n");
61	<	printf("      --scd                       scd order parameter(either --sele1, --sele2, \n                                    --sele3 are specified or --molname, \n                                    --begin, --end are specified)\n");
62	<	}
34	>	const char *gengetopt_args_info_usage = "Usage: StaticProps [OPTIONS]... [FILES]...";
35
36	+	const char *gengetopt_args_info_description = "";
37
38	<	static char *gengetopt_strdup (const char *s);
38	>	const char *gengetopt_args_info_help[] = {
39	>	"  -h, --help                    Print help and exit",
40	>	"  -V, --version                 Print version and exit",
41	>	"  -i, --input=filename          input dump file",
42	>	"  -o, --output=filename         output file name",
43	>	"  -n, --step=INT                process every n frame  (default=`1')",
44	>	"  -b, --nbins=INT               number of bins (general purpose)  \n                                  (default=`100')",
45	>	"  -x, --nbins_x=INT             number of bins in x axis  (default=`100')",
46	>	"  -y, --nbins_y=INT             number of bins in y axis  (default=`100')",
47	>	"      --nbins_z=INT             number of bins in z axis  (default=`100')",
48	>	"  -a, --nanglebins=INT          number of bins for cos(angle)  (default=`50')",
49	>	"  -c, --rcut=DOUBLE             cutoff radius (rcut)",
50	>	"      --dz=DOUBLE               slab width (dz)",
51	>	"      --length=DOUBLE           maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
52	>	"      --zlength=DOUBLE          maximum length (Defaults to 1/2 smallest length \n                                  of first frame)",
53	>	"  -z, --zoffset=DOUBLE          Where to set the zero for the slab_density \n                                  calculation  (default=`0')",
54	>	"      --sele1=selection script  select the first stuntdouble set",
55	>	"      --sele2=selection script  select the second stuntdouble set",
56	>	"      --sele3=selection script  select the third stuntdouble set",
57	>	"      --refsele=selection script\n                                select reference (use and only use with --gxyz)",
58	>	"      --comsele=selection script\n                                select stunt doubles for center-of-mass \n                                  reference point",
59	>	"      --molname=STRING          molecule name",
60	>	"      --begin=INT               begin internal index",
61	>	"      --end=INT                 end internal index",
62	>	"      --radius=DOUBLE           nanoparticle radius",
63	>	"\n Group: staticProps\n   an option of this group is required",
64	>	"      --bo                      bond order parameter (--rcut must be specified)",
65	>	"      --bor                     bond order parameter as a function of radius \n                                  (--rcut must be specified)",
66	>	"      --bad                     N(theta) bond angle density within (--rcut must \n                                  be specified)",
67	>	"      --count                   count of molecules matching selection criteria \n                                  (and associated statistics)",
68	>	"  -g, --gofr                    g(r)",
69	>	"      --gofz                    g(z)",
70	>	"      --r_theta                 g(r, cos(theta))",
71	>	"      --r_omega                 g(r, cos(omega))",
72	>	"      --r_z                     g(r, z)",
73	>	"      --theta_omega             g(cos(theta), cos(omega))",
74	>	"      --gxyz                    g(x, y, z)",
75	>	"      --twodgofr                2D g(r) (Slab width --dz must be specified)",
76	>	"  -p, --p2                      p2 order parameter (--sele1 must be specified, \n                                  --sele2 is optional)",
77	>	"      --rp2                     rp2 order parameter (--sele1 and --sele2 must \n                                  be specified)",
78	>	"  -s, --scd                     scd order parameter (either --sele1, --sele2, \n                                  --sele3 are specified or --molname, --begin, \n                                  --end are specified)",
79	>	"  -d, --density                 density plot",
80	>	"      --slab_density            slab density",
81	>	"      --p_angle                 p(cos(theta))",
82	>	"      --hxy                     hxy",
83	>	"      --rho_r                   rho of R",
84	>	"      --angle_r                 angle of R",
85	>	"      --hullvol                 hull volume of nanoparticle",
86	>	"      --rodlength               length of nanorod",
87	>	"  -Q, --tet_param               tetrahedrality order parameter",
88	>	"      --tet_param_z             tetrahedrality order parameter by zbin(--sele1 \n                                  must be specified)",
89	>	0
90	>	};
91
92	<	/* gengetopt_strdup() */
93	<	/* strdup.c replacement of strdup, which is not standard */
94	<	char *
95	<	gengetopt_strdup (const char *s)
96	<	{
72	<	char *result = (char*)malloc(strlen(s) + 1);
73	<	if (result == (char*)0)
74	<	return (char*)0;
75	<	strcpy(result, s);
76	<	return result;
77	<	}
92	>	typedef enum {ARG_NO
93	>	, ARG_STRING
94	>	, ARG_INT
95	>	, ARG_DOUBLE
96	>	} cmdline_parser_arg_type;
97
98	<	int
99	<	cmdline_parser (int argc, char * const *argv, struct gengetopt_args_info *args_info)
100	<	{
101	<	int c;        /* Character of the parsed option.  */
83	<	int missing_required_options = 0;
84	<	int staticProps_group_counter = 0;
85	<
98	>	static
99	>	void clear_given (struct gengetopt_args_info *args_info);
100	>	static
101	>	void clear_args (struct gengetopt_args_info *args_info);
102
103	+	static int
104	+	cmdline_parser_internal (int argc, char **argv, struct gengetopt_args_info *args_info,
105	+	struct cmdline_parser_params *params, const char *additional_error);
106	+
107	+	static int
108	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error);
109	+
110	+	static char *
111	+	gengetopt_strdup (const char *s);
112	+
113	+	static
114	+	void clear_given (struct gengetopt_args_info *args_info)
115	+	{
116		args_info->help_given = 0 ;
117		args_info->version_given = 0 ;
118		args_info->input_given = 0 ;
119		args_info->output_given = 0 ;
120		args_info->step_given = 0 ;
121	<	args_info->nrbins_given = 0 ;
121	>	args_info->nbins_given = 0 ;
122	>	args_info->nbins_x_given = 0 ;
123	>	args_info->nbins_y_given = 0 ;
124	>	args_info->nbins_z_given = 0 ;
125		args_info->nanglebins_given = 0 ;
126	+	args_info->rcut_given = 0 ;
127	+	args_info->dz_given = 0 ;
128		args_info->length_given = 0 ;
129	+	args_info->zlength_given = 0 ;
130	+	args_info->zoffset_given = 0 ;
131		args_info->sele1_given = 0 ;
132		args_info->sele2_given = 0 ;
133		args_info->sele3_given = 0 ;
134		args_info->refsele_given = 0 ;
135	+	args_info->comsele_given = 0 ;
136		args_info->molname_given = 0 ;
137		args_info->begin_given = 0 ;
138		args_info->end_given = 0 ;
139	+	args_info->radius_given = 0 ;
140	+	args_info->bo_given = 0 ;
141	+	args_info->bor_given = 0 ;
142	+	args_info->bad_given = 0 ;
143	+	args_info->count_given = 0 ;
144		args_info->gofr_given = 0 ;
145	+	args_info->gofz_given = 0 ;
146		args_info->r_theta_given = 0 ;
147		args_info->r_omega_given = 0 ;
148	+	args_info->r_z_given = 0 ;
149		args_info->theta_omega_given = 0 ;
150		args_info->gxyz_given = 0 ;
151	+	args_info->twodgofr_given = 0 ;
152		args_info->p2_given = 0 ;
153	+	args_info->rp2_given = 0 ;
154		args_info->scd_given = 0 ;
155	<	#define clear_args() { \
156	<	args_info->input_arg = NULL; \
157	<	args_info->output_arg = NULL; \
158	<	args_info->step_arg = 1 ;\
159	<	args_info->nrbins_arg = 100 ;\
160	<	args_info->nanglebins_arg = 50 ;\
161	<	args_info->sele1_arg = NULL; \
162	<	args_info->sele2_arg = NULL; \
163	<	args_info->sele3_arg = NULL; \
164	<	args_info->refsele_arg = NULL; \
165	<	args_info->molname_arg = NULL; \
155	>	args_info->density_given = 0 ;
156	>	args_info->slab_density_given = 0 ;
157	>	args_info->p_angle_given = 0 ;
158	>	args_info->hxy_given = 0 ;
159	>	args_info->rho_r_given = 0 ;
160	>	args_info->angle_r_given = 0 ;
161	>	args_info->hullvol_given = 0 ;
162	>	args_info->rodlength_given = 0 ;
163	>	args_info->tet_param_given = 0 ;
164	>	args_info->tet_param_z_given = 0 ;
165	>	args_info->staticProps_group_counter = 0 ;
166		}
167
168	<	clear_args();
168	>	static
169	>	void clear_args (struct gengetopt_args_info *args_info)
170	>	{
171	>	FIX_UNUSED (args_info);
172	>	args_info->input_arg = NULL;
173	>	args_info->input_orig = NULL;
174	>	args_info->output_arg = NULL;
175	>	args_info->output_orig = NULL;
176	>	args_info->step_arg = 1;
177	>	args_info->step_orig = NULL;
178	>	args_info->nbins_arg = 100;
179	>	args_info->nbins_orig = NULL;
180	>	args_info->nbins_x_arg = 100;
181	>	args_info->nbins_x_orig = NULL;
182	>	args_info->nbins_y_arg = 100;
183	>	args_info->nbins_y_orig = NULL;
184	>	args_info->nbins_z_arg = 100;
185	>	args_info->nbins_z_orig = NULL;
186	>	args_info->nanglebins_arg = 50;
187	>	args_info->nanglebins_orig = NULL;
188	>	args_info->rcut_orig = NULL;
189	>	args_info->dz_orig = NULL;
190	>	args_info->length_orig = NULL;
191	>	args_info->zlength_orig = NULL;
192	>	args_info->zoffset_arg = 0;
193	>	args_info->zoffset_orig = NULL;
194	>	args_info->sele1_arg = NULL;
195	>	args_info->sele1_orig = NULL;
196	>	args_info->sele2_arg = NULL;
197	>	args_info->sele2_orig = NULL;
198	>	args_info->sele3_arg = NULL;
199	>	args_info->sele3_orig = NULL;
200	>	args_info->refsele_arg = NULL;
201	>	args_info->refsele_orig = NULL;
202	>	args_info->comsele_arg = NULL;
203	>	args_info->comsele_orig = NULL;
204	>	args_info->molname_arg = NULL;
205	>	args_info->molname_orig = NULL;
206	>	args_info->begin_orig = NULL;
207	>	args_info->end_orig = NULL;
208	>	args_info->radius_orig = NULL;
209	>
210	>	}
211
212	+	static
213	+	void init_args_info(struct gengetopt_args_info *args_info)
214	+	{
215	+
216	+
217	+	args_info->help_help = gengetopt_args_info_help[0] ;
218	+	args_info->version_help = gengetopt_args_info_help[1] ;
219	+	args_info->input_help = gengetopt_args_info_help[2] ;
220	+	args_info->output_help = gengetopt_args_info_help[3] ;
221	+	args_info->step_help = gengetopt_args_info_help[4] ;
222	+	args_info->nbins_help = gengetopt_args_info_help[5] ;
223	+	args_info->nbins_x_help = gengetopt_args_info_help[6] ;
224	+	args_info->nbins_y_help = gengetopt_args_info_help[7] ;
225	+	args_info->nbins_z_help = gengetopt_args_info_help[8] ;
226	+	args_info->nanglebins_help = gengetopt_args_info_help[9] ;
227	+	args_info->rcut_help = gengetopt_args_info_help[10] ;
228	+	args_info->dz_help = gengetopt_args_info_help[11] ;
229	+	args_info->length_help = gengetopt_args_info_help[12] ;
230	+	args_info->zlength_help = gengetopt_args_info_help[13] ;
231	+	args_info->zoffset_help = gengetopt_args_info_help[14] ;
232	+	args_info->sele1_help = gengetopt_args_info_help[15] ;
233	+	args_info->sele2_help = gengetopt_args_info_help[16] ;
234	+	args_info->sele3_help = gengetopt_args_info_help[17] ;
235	+	args_info->refsele_help = gengetopt_args_info_help[18] ;
236	+	args_info->comsele_help = gengetopt_args_info_help[19] ;
237	+	args_info->molname_help = gengetopt_args_info_help[20] ;
238	+	args_info->begin_help = gengetopt_args_info_help[21] ;
239	+	args_info->end_help = gengetopt_args_info_help[22] ;
240	+	args_info->radius_help = gengetopt_args_info_help[23] ;
241	+	args_info->bo_help = gengetopt_args_info_help[25] ;
242	+	args_info->bor_help = gengetopt_args_info_help[26] ;
243	+	args_info->bad_help = gengetopt_args_info_help[27] ;
244	+	args_info->count_help = gengetopt_args_info_help[28] ;
245	+	args_info->gofr_help = gengetopt_args_info_help[29] ;
246	+	args_info->gofz_help = gengetopt_args_info_help[30] ;
247	+	args_info->r_theta_help = gengetopt_args_info_help[31] ;
248	+	args_info->r_omega_help = gengetopt_args_info_help[32] ;
249	+	args_info->r_z_help = gengetopt_args_info_help[33] ;
250	+	args_info->theta_omega_help = gengetopt_args_info_help[34] ;
251	+	args_info->gxyz_help = gengetopt_args_info_help[35] ;
252	+	args_info->twodgofr_help = gengetopt_args_info_help[36] ;
253	+	args_info->p2_help = gengetopt_args_info_help[37] ;
254	+	args_info->rp2_help = gengetopt_args_info_help[38] ;
255	+	args_info->scd_help = gengetopt_args_info_help[39] ;
256	+	args_info->density_help = gengetopt_args_info_help[40] ;
257	+	args_info->slab_density_help = gengetopt_args_info_help[41] ;
258	+	args_info->p_angle_help = gengetopt_args_info_help[42] ;
259	+	args_info->hxy_help = gengetopt_args_info_help[43] ;
260	+	args_info->rho_r_help = gengetopt_args_info_help[44] ;
261	+	args_info->angle_r_help = gengetopt_args_info_help[45] ;
262	+	args_info->hullvol_help = gengetopt_args_info_help[46] ;
263	+	args_info->rodlength_help = gengetopt_args_info_help[47] ;
264	+	args_info->tet_param_help = gengetopt_args_info_help[48] ;
265	+	args_info->tet_param_z_help = gengetopt_args_info_help[49] ;
266	+
267	+	}
268	+
269	+	void
270	+	cmdline_parser_print_version (void)
271	+	{
272	+	printf ("%s %s\n",
273	+	(strlen(CMDLINE_PARSER_PACKAGE_NAME) ? CMDLINE_PARSER_PACKAGE_NAME : CMDLINE_PARSER_PACKAGE),
274	+	CMDLINE_PARSER_VERSION);
275	+	}
276	+
277	+	static void print_help_common(void) {
278	+	cmdline_parser_print_version ();
279	+
280	+	if (strlen(gengetopt_args_info_purpose) > 0)
281	+	printf("\n%s\n", gengetopt_args_info_purpose);
282	+
283	+	if (strlen(gengetopt_args_info_usage) > 0)
284	+	printf("\n%s\n", gengetopt_args_info_usage);
285	+
286	+	printf("\n");
287	+
288	+	if (strlen(gengetopt_args_info_description) > 0)
289	+	printf("%s\n\n", gengetopt_args_info_description);
290	+	}
291	+
292	+	void
293	+	cmdline_parser_print_help (void)
294	+	{
295	+	int i = 0;
296	+	print_help_common();
297	+	while (gengetopt_args_info_help[i])
298	+	printf("%s\n", gengetopt_args_info_help[i++]);
299	+	}
300	+
301	+	void
302	+	cmdline_parser_init (struct gengetopt_args_info *args_info)
303	+	{
304	+	clear_given (args_info);
305	+	clear_args (args_info);
306	+	init_args_info (args_info);
307	+
308	+	args_info->inputs = 0;
309	+	args_info->inputs_num = 0;
310	+	}
311	+
312	+	void
313	+	cmdline_parser_params_init(struct cmdline_parser_params *params)
314	+	{
315	+	if (params)
316	+	{
317	+	params->override = 0;
318	+	params->initialize = 1;
319	+	params->check_required = 1;
320	+	params->check_ambiguity = 0;
321	+	params->print_errors = 1;
322	+	}
323	+	}
324	+
325	+	struct cmdline_parser_params *
326	+	cmdline_parser_params_create(void)
327	+	{
328	+	struct cmdline_parser_params *params =
329	+	(struct cmdline_parser_params *)malloc(sizeof(struct cmdline_parser_params));
330	+	cmdline_parser_params_init(params);
331	+	return params;
332	+	}
333	+
334	+	static void
335	+	free_string_field (char **s)
336	+	{
337	+	if (*s)
338	+	{
339	+	free (*s);
340	+	*s = 0;
341	+	}
342	+	}
343	+
344	+
345	+	static void
346	+	cmdline_parser_release (struct gengetopt_args_info *args_info)
347	+	{
348	+	unsigned int i;
349	+	free_string_field (&(args_info->input_arg));
350	+	free_string_field (&(args_info->input_orig));
351	+	free_string_field (&(args_info->output_arg));
352	+	free_string_field (&(args_info->output_orig));
353	+	free_string_field (&(args_info->step_orig));
354	+	free_string_field (&(args_info->nbins_orig));
355	+	free_string_field (&(args_info->nbins_x_orig));
356	+	free_string_field (&(args_info->nbins_y_orig));
357	+	free_string_field (&(args_info->nbins_z_orig));
358	+	free_string_field (&(args_info->nanglebins_orig));
359	+	free_string_field (&(args_info->rcut_orig));
360	+	free_string_field (&(args_info->dz_orig));
361	+	free_string_field (&(args_info->length_orig));
362	+	free_string_field (&(args_info->zlength_orig));
363	+	free_string_field (&(args_info->zoffset_orig));
364	+	free_string_field (&(args_info->sele1_arg));
365	+	free_string_field (&(args_info->sele1_orig));
366	+	free_string_field (&(args_info->sele2_arg));
367	+	free_string_field (&(args_info->sele2_orig));
368	+	free_string_field (&(args_info->sele3_arg));
369	+	free_string_field (&(args_info->sele3_orig));
370	+	free_string_field (&(args_info->refsele_arg));
371	+	free_string_field (&(args_info->refsele_orig));
372	+	free_string_field (&(args_info->comsele_arg));
373	+	free_string_field (&(args_info->comsele_orig));
374	+	free_string_field (&(args_info->molname_arg));
375	+	free_string_field (&(args_info->molname_orig));
376	+	free_string_field (&(args_info->begin_orig));
377	+	free_string_field (&(args_info->end_orig));
378	+	free_string_field (&(args_info->radius_orig));
379	+
380	+
381	+	for (i = 0; i < args_info->inputs_num; ++i)
382	+	free (args_info->inputs [i]);
383	+
384	+	if (args_info->inputs_num)
385	+	free (args_info->inputs);
386	+
387	+	clear_given (args_info);
388	+	}
389	+
390	+
391	+	static void
392	+	write_into_file(FILE *outfile, const char *opt, const char *arg, const char *values[])
393	+	{
394	+	FIX_UNUSED (values);
395	+	if (arg) {
396	+	fprintf(outfile, "%s=\"%s\"\n", opt, arg);
397	+	} else {
398	+	fprintf(outfile, "%s\n", opt);
399	+	}
400	+	}
401	+
402	+
403	+	int
404	+	cmdline_parser_dump(FILE *outfile, struct gengetopt_args_info *args_info)
405	+	{
406	+	int i = 0;
407	+
408	+	if (!outfile)
409	+	{
410	+	fprintf (stderr, "%s: cannot dump options to stream\n", CMDLINE_PARSER_PACKAGE);
411	+	return EXIT_FAILURE;
412	+	}
413	+
414	+	if (args_info->help_given)
415	+	write_into_file(outfile, "help", 0, 0 );
416	+	if (args_info->version_given)
417	+	write_into_file(outfile, "version", 0, 0 );
418	+	if (args_info->input_given)
419	+	write_into_file(outfile, "input", args_info->input_orig, 0);
420	+	if (args_info->output_given)
421	+	write_into_file(outfile, "output", args_info->output_orig, 0);
422	+	if (args_info->step_given)
423	+	write_into_file(outfile, "step", args_info->step_orig, 0);
424	+	if (args_info->nbins_given)
425	+	write_into_file(outfile, "nbins", args_info->nbins_orig, 0);
426	+	if (args_info->nbins_x_given)
427	+	write_into_file(outfile, "nbins_x", args_info->nbins_x_orig, 0);
428	+	if (args_info->nbins_y_given)
429	+	write_into_file(outfile, "nbins_y", args_info->nbins_y_orig, 0);
430	+	if (args_info->nbins_z_given)
431	+	write_into_file(outfile, "nbins_z", args_info->nbins_z_orig, 0);
432	+	if (args_info->nanglebins_given)
433	+	write_into_file(outfile, "nanglebins", args_info->nanglebins_orig, 0);
434	+	if (args_info->rcut_given)
435	+	write_into_file(outfile, "rcut", args_info->rcut_orig, 0);
436	+	if (args_info->dz_given)
437	+	write_into_file(outfile, "dz", args_info->dz_orig, 0);
438	+	if (args_info->length_given)
439	+	write_into_file(outfile, "length", args_info->length_orig, 0);
440	+	if (args_info->zlength_given)
441	+	write_into_file(outfile, "zlength", args_info->zlength_orig, 0);
442	+	if (args_info->zoffset_given)
443	+	write_into_file(outfile, "zoffset", args_info->zoffset_orig, 0);
444	+	if (args_info->sele1_given)
445	+	write_into_file(outfile, "sele1", args_info->sele1_orig, 0);
446	+	if (args_info->sele2_given)
447	+	write_into_file(outfile, "sele2", args_info->sele2_orig, 0);
448	+	if (args_info->sele3_given)
449	+	write_into_file(outfile, "sele3", args_info->sele3_orig, 0);
450	+	if (args_info->refsele_given)
451	+	write_into_file(outfile, "refsele", args_info->refsele_orig, 0);
452	+	if (args_info->comsele_given)
453	+	write_into_file(outfile, "comsele", args_info->comsele_orig, 0);
454	+	if (args_info->molname_given)
455	+	write_into_file(outfile, "molname", args_info->molname_orig, 0);
456	+	if (args_info->begin_given)
457	+	write_into_file(outfile, "begin", args_info->begin_orig, 0);
458	+	if (args_info->end_given)
459	+	write_into_file(outfile, "end", args_info->end_orig, 0);
460	+	if (args_info->radius_given)
461	+	write_into_file(outfile, "radius", args_info->radius_orig, 0);
462	+	if (args_info->bo_given)
463	+	write_into_file(outfile, "bo", 0, 0 );
464	+	if (args_info->bor_given)
465	+	write_into_file(outfile, "bor", 0, 0 );
466	+	if (args_info->bad_given)
467	+	write_into_file(outfile, "bad", 0, 0 );
468	+	if (args_info->count_given)
469	+	write_into_file(outfile, "count", 0, 0 );
470	+	if (args_info->gofr_given)
471	+	write_into_file(outfile, "gofr", 0, 0 );
472	+	if (args_info->gofz_given)
473	+	write_into_file(outfile, "gofz", 0, 0 );
474	+	if (args_info->r_theta_given)
475	+	write_into_file(outfile, "r_theta", 0, 0 );
476	+	if (args_info->r_omega_given)
477	+	write_into_file(outfile, "r_omega", 0, 0 );
478	+	if (args_info->r_z_given)
479	+	write_into_file(outfile, "r_z", 0, 0 );
480	+	if (args_info->theta_omega_given)
481	+	write_into_file(outfile, "theta_omega", 0, 0 );
482	+	if (args_info->gxyz_given)
483	+	write_into_file(outfile, "gxyz", 0, 0 );
484	+	if (args_info->twodgofr_given)
485	+	write_into_file(outfile, "twodgofr", 0, 0 );
486	+	if (args_info->p2_given)
487	+	write_into_file(outfile, "p2", 0, 0 );
488	+	if (args_info->rp2_given)
489	+	write_into_file(outfile, "rp2", 0, 0 );
490	+	if (args_info->scd_given)
491	+	write_into_file(outfile, "scd", 0, 0 );
492	+	if (args_info->density_given)
493	+	write_into_file(outfile, "density", 0, 0 );
494	+	if (args_info->slab_density_given)
495	+	write_into_file(outfile, "slab_density", 0, 0 );
496	+	if (args_info->p_angle_given)
497	+	write_into_file(outfile, "p_angle", 0, 0 );
498	+	if (args_info->hxy_given)
499	+	write_into_file(outfile, "hxy", 0, 0 );
500	+	if (args_info->rho_r_given)
501	+	write_into_file(outfile, "rho_r", 0, 0 );
502	+	if (args_info->angle_r_given)
503	+	write_into_file(outfile, "angle_r", 0, 0 );
504	+	if (args_info->hullvol_given)
505	+	write_into_file(outfile, "hullvol", 0, 0 );
506	+	if (args_info->rodlength_given)
507	+	write_into_file(outfile, "rodlength", 0, 0 );
508	+	if (args_info->tet_param_given)
509	+	write_into_file(outfile, "tet_param", 0, 0 );
510	+	if (args_info->tet_param_z_given)
511	+	write_into_file(outfile, "tet_param_z", 0, 0 );
512	+
513	+
514	+	i = EXIT_SUCCESS;
515	+	return i;
516	+	}
517	+
518	+	int
519	+	cmdline_parser_file_save(const char *filename, struct gengetopt_args_info *args_info)
520	+	{
521	+	FILE *outfile;
522	+	int i = 0;
523	+
524	+	outfile = fopen(filename, "w");
525	+
526	+	if (!outfile)
527	+	{
528	+	fprintf (stderr, "%s: cannot open file for writing: %s\n", CMDLINE_PARSER_PACKAGE, filename);
529	+	return EXIT_FAILURE;
530	+	}
531	+
532	+	i = cmdline_parser_dump(outfile, args_info);
533	+	fclose (outfile);
534	+
535	+	return i;
536	+	}
537	+
538	+	void
539	+	cmdline_parser_free (struct gengetopt_args_info *args_info)
540	+	{
541	+	cmdline_parser_release (args_info);
542	+	}
543	+
544	+	/** @brief replacement of strdup, which is not standard */
545	+	char *
546	+	gengetopt_strdup (const char *s)
547	+	{
548	+	char *result = 0;
549	+	if (!s)
550	+	return result;
551	+
552	+	result = (char*)malloc(strlen(s) + 1);
553	+	if (result == (char*)0)
554	+	return (char*)0;
555	+	strcpy(result, s);
556	+	return result;
557	+	}
558	+
559	+	static void
560	+	reset_group_staticProps(struct gengetopt_args_info *args_info)
561	+	{
562	+	if (! args_info->staticProps_group_counter)
563	+	return;
564	+
565	+	args_info->bo_given = 0 ;
566	+	args_info->bor_given = 0 ;
567	+	args_info->bad_given = 0 ;
568	+	args_info->count_given = 0 ;
569	+	args_info->gofr_given = 0 ;
570	+	args_info->gofz_given = 0 ;
571	+	args_info->r_theta_given = 0 ;
572	+	args_info->r_omega_given = 0 ;
573	+	args_info->r_z_given = 0 ;
574	+	args_info->theta_omega_given = 0 ;
575	+	args_info->gxyz_given = 0 ;
576	+	args_info->twodgofr_given = 0 ;
577	+	args_info->p2_given = 0 ;
578	+	args_info->rp2_given = 0 ;
579	+	args_info->scd_given = 0 ;
580	+	args_info->density_given = 0 ;
581	+	args_info->slab_density_given = 0 ;
582	+	args_info->p_angle_given = 0 ;
583	+	args_info->hxy_given = 0 ;
584	+	args_info->rho_r_given = 0 ;
585	+	args_info->angle_r_given = 0 ;
586	+	args_info->hullvol_given = 0 ;
587	+	args_info->rodlength_given = 0 ;
588	+	args_info->tet_param_given = 0 ;
589	+	args_info->tet_param_z_given = 0 ;
590	+
591	+	args_info->staticProps_group_counter = 0;
592	+	}
593	+
594	+	int
595	+	cmdline_parser (int argc, char **argv, struct gengetopt_args_info *args_info)
596	+	{
597	+	return cmdline_parser2 (argc, argv, args_info, 0, 1, 1);
598	+	}
599	+
600	+	int
601	+	cmdline_parser_ext (int argc, char **argv, struct gengetopt_args_info *args_info,
602	+	struct cmdline_parser_params *params)
603	+	{
604	+	int result;
605	+	result = cmdline_parser_internal (argc, argv, args_info, params, 0);
606	+
607	+	if (result == EXIT_FAILURE)
608	+	{
609	+	cmdline_parser_free (args_info);
610	+	exit (EXIT_FAILURE);
611	+	}
612	+
613	+	return result;
614	+	}
615	+
616	+	int
617	+	cmdline_parser2 (int argc, char **argv, struct gengetopt_args_info *args_info, int override, int initialize, int check_required)
618	+	{
619	+	int result;
620	+	struct cmdline_parser_params params;
621	+
622	+	params.override = override;
623	+	params.initialize = initialize;
624	+	params.check_required = check_required;
625	+	params.check_ambiguity = 0;
626	+	params.print_errors = 1;
627	+
628	+	result = cmdline_parser_internal (argc, argv, args_info, &params, 0);
629	+
630	+	if (result == EXIT_FAILURE)
631	+	{
632	+	cmdline_parser_free (args_info);
633	+	exit (EXIT_FAILURE);
634	+	}
635	+
636	+	return result;
637	+	}
638	+
639	+	int
640	+	cmdline_parser_required (struct gengetopt_args_info *args_info, const char *prog_name)
641	+	{
642	+	int result = EXIT_SUCCESS;
643	+
644	+	if (cmdline_parser_required2(args_info, prog_name, 0) > 0)
645	+	result = EXIT_FAILURE;
646	+
647	+	if (result == EXIT_FAILURE)
648	+	{
649	+	cmdline_parser_free (args_info);
650	+	exit (EXIT_FAILURE);
651	+	}
652	+
653	+	return result;
654	+	}
655	+
656	+	int
657	+	cmdline_parser_required2 (struct gengetopt_args_info *args_info, const char *prog_name, const char *additional_error)
658	+	{
659	+	int error = 0;
660	+	FIX_UNUSED (additional_error);
661	+
662	+	/* checks for required options */
663	+	if (! args_info->input_given)
664	+	{
665	+	fprintf (stderr, "%s: '--input' ('-i') option required%s\n", prog_name, (additional_error ? additional_error : ""));
666	+	error = 1;
667	+	}
668	+
669	+	if (args_info->staticProps_group_counter == 0)
670	+	{
671	+	fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", prog_name, args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
672	+	error = 1;
673	+	}
674	+
675	+
676	+	/* checks for dependences among options */
677	+
678	+	return error;
679	+	}
680	+
681	+
682	+	static char *package_name = 0;
683	+
684	+	/**
685	+	* @brief updates an option
686	+	* @param field the generic pointer to the field to update
687	+	* @param orig_field the pointer to the orig field
688	+	* @param field_given the pointer to the number of occurrence of this option
689	+	* @param prev_given the pointer to the number of occurrence already seen
690	+	* @param value the argument for this option (if null no arg was specified)
691	+	* @param possible_values the possible values for this option (if specified)
692	+	* @param default_value the default value (in case the option only accepts fixed values)
693	+	* @param arg_type the type of this option
694	+	* @param check_ambiguity @see cmdline_parser_params.check_ambiguity
695	+	* @param override @see cmdline_parser_params.override
696	+	* @param no_free whether to free a possible previous value
697	+	* @param multiple_option whether this is a multiple option
698	+	* @param long_opt the corresponding long option
699	+	* @param short_opt the corresponding short option (or '-' if none)
700	+	* @param additional_error possible further error specification
701	+	*/
702	+	static
703	+	int update_arg(void *field, char **orig_field,
704	+	unsigned int *field_given, unsigned int *prev_given,
705	+	char *value, const char *possible_values[],
706	+	const char *default_value,
707	+	cmdline_parser_arg_type arg_type,
708	+	int check_ambiguity, int override,
709	+	int no_free, int multiple_option,
710	+	const char *long_opt, char short_opt,
711	+	const char *additional_error)
712	+	{
713	+	char *stop_char = 0;
714	+	const char *val = value;
715	+	int found;
716	+	char **string_field;
717	+	FIX_UNUSED (field);
718	+
719	+	stop_char = 0;
720	+	found = 0;
721	+
722	+	if (!multiple_option && prev_given && (*prev_given || (check_ambiguity && *field_given)))
723	+	{
724	+	if (short_opt != '-')
725	+	fprintf (stderr, "%s: `--%s' (`-%c') option given more than once%s\n",
726	+	package_name, long_opt, short_opt,
727	+	(additional_error ? additional_error : ""));
728	+	else
729	+	fprintf (stderr, "%s: `--%s' option given more than once%s\n",
730	+	package_name, long_opt,
731	+	(additional_error ? additional_error : ""));
732	+	return 1; /* failure */
733	+	}
734	+
735	+	FIX_UNUSED (default_value);
736	+
737	+	if (field_given && *field_given && ! override)
738	+	return 0;
739	+	if (prev_given)
740	+	(*prev_given)++;
741	+	if (field_given)
742	+	(*field_given)++;
743	+	if (possible_values)
744	+	val = possible_values[found];
745	+
746	+	switch(arg_type) {
747	+	case ARG_INT:
748	+	if (val) *((int *)field) = strtol (val, &stop_char, 0);
749	+	break;
750	+	case ARG_DOUBLE:
751	+	if (val) *((double *)field) = strtod (val, &stop_char);
752	+	break;
753	+	case ARG_STRING:
754	+	if (val) {
755	+	string_field = (char **)field;
756	+	if (!no_free && *string_field)
757	+	free (*string_field); /* free previous string */
758	+	*string_field = gengetopt_strdup (val);
759	+	}
760	+	break;
761	+	default:
762	+	break;
763	+	};
764	+
765	+	/* check numeric conversion */
766	+	switch(arg_type) {
767	+	case ARG_INT:
768	+	case ARG_DOUBLE:
769	+	if (val && !(stop_char && *stop_char == '\0')) {
770	+	fprintf(stderr, "%s: invalid numeric value: %s\n", package_name, val);
771	+	return 1; /* failure */
772	+	}
773	+	break;
774	+	default:
775	+	;
776	+	};
777	+
778	+	/* store the original value */
779	+	switch(arg_type) {
780	+	case ARG_NO:
781	+	break;
782	+	default:
783	+	if (value && orig_field) {
784	+	if (no_free) {
785	+	*orig_field = value;
786	+	} else {
787	+	if (*orig_field)
788	+	free (*orig_field); /* free previous string */
789	+	*orig_field = gengetopt_strdup (value);
790	+	}
791	+	}
792	+	};
793	+
794	+	return 0; /* OK */
795	+	}
796	+
797	+
798	+	int
799	+	cmdline_parser_internal (
800	+	int argc, char **argv, struct gengetopt_args_info *args_info,
801	+	struct cmdline_parser_params *params, const char *additional_error)
802	+	{
803	+	int c;        /* Character of the parsed option.  */
804	+
805	+	int error = 0;
806	+	struct gengetopt_args_info local_args_info;
807	+
808	+	int override;
809	+	int initialize;
810	+	int check_required;
811	+	int check_ambiguity;
812	+
813	+	package_name = argv[0];
814	+
815	+	override = params->override;
816	+	initialize = params->initialize;
817	+	check_required = params->check_required;
818	+	check_ambiguity = params->check_ambiguity;
819	+
820	+	if (initialize)
821	+	cmdline_parser_init (args_info);
822	+
823	+	cmdline_parser_init (&local_args_info);
824	+
825		optarg = 0;
826	<	optind = 1;
827	<	opterr = 1;
826	>	optind = 0;
827	>	opterr = params->print_errors;
828		optopt = '?';
829
830		while (1)
831		{
832		int option_index = 0;
132	–	char *stop_char;
833
834		static struct option long_options[] = {
835		{ "help",       0, NULL, 'h' },
#	Line 137 | Line 837 | cmdline_parser (int argc, char * const *argv, struct g
837		{ "input",      1, NULL, 'i' },
838		{ "output",     1, NULL, 'o' },
839		{ "step",       1, NULL, 'n' },
840	<	{ "nrbins",     1, NULL, 'r' },
840	>	{ "nbins",      1, NULL, 'b' },
841	>	{ "nbins_x",    1, NULL, 'x' },
842	>	{ "nbins_y",    1, NULL, 'y' },
843	>	{ "nbins_z",    1, NULL, 0 },
844		{ "nanglebins", 1, NULL, 'a' },
845	<	{ "length",     1, NULL, 'l' },
845	>	{ "rcut",       1, NULL, 'c' },
846	>	{ "dz", 1, NULL, 0 },
847	>	{ "length",     1, NULL, 0 },
848	>	{ "zlength",    1, NULL, 0 },
849	>	{ "zoffset",    1, NULL, 'z' },
850		{ "sele1",      1, NULL, 0 },
851		{ "sele2",      1, NULL, 0 },
852		{ "sele3",      1, NULL, 0 },
853		{ "refsele",    1, NULL, 0 },
854	+	{ "comsele",    1, NULL, 0 },
855		{ "molname",    1, NULL, 0 },
856		{ "begin",      1, NULL, 0 },
857		{ "end",        1, NULL, 0 },
858	<	{ "gofr",       0, NULL, 0 },
858	>	{ "radius",     1, NULL, 0 },
859	>	{ "bo", 0, NULL, 0 },
860	>	{ "bor",        0, NULL, 0 },
861	>	{ "bad",        0, NULL, 0 },
862	>	{ "count",      0, NULL, 0 },
863	>	{ "gofr",       0, NULL, 'g' },
864	>	{ "gofz",       0, NULL, 0 },
865		{ "r_theta",    0, NULL, 0 },
866		{ "r_omega",    0, NULL, 0 },
867	+	{ "r_z",        0, NULL, 0 },
868		{ "theta_omega",        0, NULL, 0 },
869		{ "gxyz",       0, NULL, 0 },
870	<	{ "p2", 0, NULL, 0 },
871	<	{ "scd",        0, NULL, 0 },
872	<	{ NULL, 0, NULL, 0 }
870	>	{ "twodgofr",   0, NULL, 0 },
871	>	{ "p2", 0, NULL, 'p' },
872	>	{ "rp2",        0, NULL, 0 },
873	>	{ "scd",        0, NULL, 's' },
874	>	{ "density",    0, NULL, 'd' },
875	>	{ "slab_density",       0, NULL, 0 },
876	>	{ "p_angle",    0, NULL, 0 },
877	>	{ "hxy",        0, NULL, 0 },
878	>	{ "rho_r",      0, NULL, 0 },
879	>	{ "angle_r",    0, NULL, 0 },
880	>	{ "hullvol",    0, NULL, 0 },
881	>	{ "rodlength",  0, NULL, 0 },
882	>	{ "tet_param",  0, NULL, 'Q' },
883	>	{ "tet_param_z",        0, NULL, 0 },
884	>	{ 0,  0, 0, 0 }
885		};
886
887	<	stop_char = 0;
161	<	c = getopt_long (argc, argv, "hVi:o:n:r:a:l:", long_options, &option_index);
887	>	c = getopt_long (argc, argv, "hVi:o:n:b:x:y:a:c:z:gpsdQ", long_options, &option_index);
888
889		if (c == -1) break;       /* Exit from `while (1)' loop.  */
890
891		switch (c)
892		{
893		case 'h':       /* Print help and exit.  */
168	–	clear_args ();
894		cmdline_parser_print_help ();
895	+	cmdline_parser_free (&local_args_info);
896		exit (EXIT_SUCCESS);
897
898		case 'V':       /* Print version and exit.  */
173	–	clear_args ();
899		cmdline_parser_print_version ();
900	+	cmdline_parser_free (&local_args_info);
901		exit (EXIT_SUCCESS);
902
903		case 'i':       /* input dump file.  */
904	<	if (args_info->input_given)
905	<	{
906	<	fprintf (stderr, "%s: `--input' (`-i') option given more than once\n", CMDLINE_PARSER_PACKAGE);
907	<	clear_args ();
908	<	exit (EXIT_FAILURE);
909	<	}
910	<	args_info->input_given = 1;
911	<	args_info->input_arg = gengetopt_strdup (optarg);
912	<	break;
913	<
904	>
905	>
906	>	if (update_arg( (void *)&(args_info->input_arg),
907	>	&(args_info->input_orig), &(args_info->input_given),
908	>	&(local_args_info.input_given), optarg, 0, 0, ARG_STRING,
909	>	check_ambiguity, override, 0, 0,
910	>	"input", 'i',
911	>	additional_error))
912	>	goto failure;
913	>
914	>	break;
915		case 'o':       /* output file name.  */
916	<	if (args_info->output_given)
917	<	{
918	<	fprintf (stderr, "%s: `--output' (`-o') option given more than once\n", CMDLINE_PARSER_PACKAGE);
919	<	clear_args ();
920	<	exit (EXIT_FAILURE);
921	<	}
922	<	args_info->output_given = 1;
923	<	args_info->output_arg = gengetopt_strdup (optarg);
916	>
917	>
918	>	if (update_arg( (void *)&(args_info->output_arg),
919	>	&(args_info->output_orig), &(args_info->output_given),
920	>	&(local_args_info.output_given), optarg, 0, 0, ARG_STRING,
921	>	check_ambiguity, override, 0, 0,
922	>	"output", 'o',
923	>	additional_error))
924	>	goto failure;
925	>
926		break;
198	–
927		case 'n':       /* process every n frame.  */
928	<	if (args_info->step_given)
929	<	{
930	<	fprintf (stderr, "%s: `--step' (`-n') option given more than once\n", CMDLINE_PARSER_PACKAGE);
931	<	clear_args ();
932	<	exit (EXIT_FAILURE);
933	<	}
934	<	args_info->step_given = 1;
935	<	args_info->step_arg = strtol (optarg,&stop_char,0);
928	>
929	>
930	>	if (update_arg( (void *)&(args_info->step_arg),
931	>	&(args_info->step_orig), &(args_info->step_given),
932	>	&(local_args_info.step_given), optarg, 0, "1", ARG_INT,
933	>	check_ambiguity, override, 0, 0,
934	>	"step", 'n',
935	>	additional_error))
936	>	goto failure;
937	>
938		break;
939	<
940	<	case 'r':       /* number of bins for distance.  */
941	<	if (args_info->nrbins_given)
942	<	{
943	<	fprintf (stderr, "%s: `--nrbins' (`-r') option given more than once\n", CMDLINE_PARSER_PACKAGE);
944	<	clear_args ();
945	<	exit (EXIT_FAILURE);
946	<	}
947	<	args_info->nrbins_given = 1;
948	<	args_info->nrbins_arg = strtol (optarg,&stop_char,0);
939	>	case 'b':       /* number of bins (general purpose).  */
940	>
941	>
942	>	if (update_arg( (void *)&(args_info->nbins_arg),
943	>	&(args_info->nbins_orig), &(args_info->nbins_given),
944	>	&(local_args_info.nbins_given), optarg, 0, "100", ARG_INT,
945	>	check_ambiguity, override, 0, 0,
946	>	"nbins", 'b',
947	>	additional_error))
948	>	goto failure;
949	>
950		break;
951	<
951	>	case 'x':       /* number of bins in x axis.  */
952	>
953	>
954	>	if (update_arg( (void *)&(args_info->nbins_x_arg),
955	>	&(args_info->nbins_x_orig), &(args_info->nbins_x_given),
956	>	&(local_args_info.nbins_x_given), optarg, 0, "100", ARG_INT,
957	>	check_ambiguity, override, 0, 0,
958	>	"nbins_x", 'x',
959	>	additional_error))
960	>	goto failure;
961	>
962	>	break;
963	>	case 'y':       /* number of bins in y axis.  */
964	>
965	>
966	>	if (update_arg( (void *)&(args_info->nbins_y_arg),
967	>	&(args_info->nbins_y_orig), &(args_info->nbins_y_given),
968	>	&(local_args_info.nbins_y_given), optarg, 0, "100", ARG_INT,
969	>	check_ambiguity, override, 0, 0,
970	>	"nbins_y", 'y',
971	>	additional_error))
972	>	goto failure;
973	>
974	>	break;
975		case 'a':       /* number of bins for cos(angle).  */
976	<	if (args_info->nanglebins_given)
977	<	{
978	<	fprintf (stderr, "%s: `--nanglebins' (`-a') option given more than once\n", CMDLINE_PARSER_PACKAGE);
979	<	clear_args ();
980	<	exit (EXIT_FAILURE);
981	<	}
982	<	args_info->nanglebins_given = 1;
983	<	args_info->nanglebins_arg = strtol (optarg,&stop_char,0);
976	>
977	>
978	>	if (update_arg( (void *)&(args_info->nanglebins_arg),
979	>	&(args_info->nanglebins_orig), &(args_info->nanglebins_given),
980	>	&(local_args_info.nanglebins_given), optarg, 0, "50", ARG_INT,
981	>	check_ambiguity, override, 0, 0,
982	>	"nanglebins", 'a',
983	>	additional_error))
984	>	goto failure;
985	>
986		break;
987	<
988	<	case 'l':       /* maximum length (Defaults to 1/2 smallest length of first frame).  */
989	<	if (args_info->length_given)
990	<	{
991	<	fprintf (stderr, "%s: `--length' (`-l') option given more than once\n", CMDLINE_PARSER_PACKAGE);
992	<	clear_args ();
993	<	exit (EXIT_FAILURE);
994	<	}
995	<	args_info->length_given = 1;
996	<	args_info->length_arg = strtod (optarg, NULL);
987	>	case 'c':       /* cutoff radius (rcut).  */
988	>
989	>
990	>	if (update_arg( (void *)&(args_info->rcut_arg),
991	>	&(args_info->rcut_orig), &(args_info->rcut_given),
992	>	&(local_args_info.rcut_given), optarg, 0, 0, ARG_DOUBLE,
993	>	check_ambiguity, override, 0, 0,
994	>	"rcut", 'c',
995	>	additional_error))
996	>	goto failure;
997	>
998		break;
999	+	case 'z':       /* Where to set the zero for the slab_density calculation.  */
1000	+
1001	+
1002	+	if (update_arg( (void *)&(args_info->zoffset_arg),
1003	+	&(args_info->zoffset_orig), &(args_info->zoffset_given),
1004	+	&(local_args_info.zoffset_given), optarg, 0, "0", ARG_DOUBLE,
1005	+	check_ambiguity, override, 0, 0,
1006	+	"zoffset", 'z',
1007	+	additional_error))
1008	+	goto failure;
1009	+
1010	+	break;
1011	+	case 'g':       /* g(r).  */
1012	+
1013	+	if (args_info->staticProps_group_counter && override)
1014	+	reset_group_staticProps (args_info);
1015	+	args_info->staticProps_group_counter += 1;
1016	+
1017	+	if (update_arg( 0 ,
1018	+	0 , &(args_info->gofr_given),
1019	+	&(local_args_info.gofr_given), optarg, 0, 0, ARG_NO,
1020	+	check_ambiguity, override, 0, 0,
1021	+	"gofr", 'g',
1022	+	additional_error))
1023	+	goto failure;
1024	+
1025	+	break;
1026	+	case 'p':       /* p2 order parameter (--sele1 must be specified, --sele2 is optional).  */
1027	+
1028	+	if (args_info->staticProps_group_counter && override)
1029	+	reset_group_staticProps (args_info);
1030	+	args_info->staticProps_group_counter += 1;
1031	+
1032	+	if (update_arg( 0 ,
1033	+	0 , &(args_info->p2_given),
1034	+	&(local_args_info.p2_given), optarg, 0, 0, ARG_NO,
1035	+	check_ambiguity, override, 0, 0,
1036	+	"p2", 'p',
1037	+	additional_error))
1038	+	goto failure;
1039	+
1040	+	break;
1041	+	case 's':       /* scd order parameter (either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1042	+
1043	+	if (args_info->staticProps_group_counter && override)
1044	+	reset_group_staticProps (args_info);
1045	+	args_info->staticProps_group_counter += 1;
1046	+
1047	+	if (update_arg( 0 ,
1048	+	0 , &(args_info->scd_given),
1049	+	&(local_args_info.scd_given), optarg, 0, 0, ARG_NO,
1050	+	check_ambiguity, override, 0, 0,
1051	+	"scd", 's',
1052	+	additional_error))
1053	+	goto failure;
1054	+
1055	+	break;
1056	+	case 'd':       /* density plot.  */
1057	+
1058	+	if (args_info->staticProps_group_counter && override)
1059	+	reset_group_staticProps (args_info);
1060	+	args_info->staticProps_group_counter += 1;
1061	+
1062	+	if (update_arg( 0 ,
1063	+	0 , &(args_info->density_given),
1064	+	&(local_args_info.density_given), optarg, 0, 0, ARG_NO,
1065	+	check_ambiguity, override, 0, 0,
1066	+	"density", 'd',
1067	+	additional_error))
1068	+	goto failure;
1069	+
1070	+	break;
1071	+	case 'Q':       /* tetrahedrality order parameter.  */
1072	+
1073	+	if (args_info->staticProps_group_counter && override)
1074	+	reset_group_staticProps (args_info);
1075	+	args_info->staticProps_group_counter += 1;
1076	+
1077	+	if (update_arg( 0 ,
1078	+	0 , &(args_info->tet_param_given),
1079	+	&(local_args_info.tet_param_given), optarg, 0, 0, ARG_NO,
1080	+	check_ambiguity, override, 0, 0,
1081	+	"tet_param", 'Q',
1082	+	additional_error))
1083	+	goto failure;
1084	+
1085	+	break;
1086
243	–
1087		case 0: /* Long option with no short option */
1088	<	/* select the first stuntdouble set.  */
1089	<	if (strcmp (long_options[option_index].name, "sele1") == 0)
1088	>	/* number of bins in z axis.  */
1089	>	if (strcmp (long_options[option_index].name, "nbins_z") == 0)
1090		{
1091	<	if (args_info->sele1_given)
1092	<	{
1093	<	fprintf (stderr, "%s: `--sele1' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1094	<	clear_args ();
1095	<	exit (EXIT_FAILURE);
1096	<	}
1097	<	args_info->sele1_given = 1;
1098	<	args_info->sele1_arg = gengetopt_strdup (optarg);
1099	<	break;
1091	>
1092	>
1093	>	if (update_arg( (void *)&(args_info->nbins_z_arg),
1094	>	&(args_info->nbins_z_orig), &(args_info->nbins_z_given),
1095	>	&(local_args_info.nbins_z_given), optarg, 0, "100", ARG_INT,
1096	>	check_ambiguity, override, 0, 0,
1097	>	"nbins_z", '-',
1098	>	additional_error))
1099	>	goto failure;
1100	>
1101		}
1102	+	/* slab width (dz).  */
1103	+	else if (strcmp (long_options[option_index].name, "dz") == 0)
1104	+	{
1105
1106	+
1107	+	if (update_arg( (void *)&(args_info->dz_arg),
1108	+	&(args_info->dz_orig), &(args_info->dz_given),
1109	+	&(local_args_info.dz_given), optarg, 0, 0, ARG_DOUBLE,
1110	+	check_ambiguity, override, 0, 0,
1111	+	"dz", '-',
1112	+	additional_error))
1113	+	goto failure;
1114	+
1115	+	}
1116	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1117	+	else if (strcmp (long_options[option_index].name, "length") == 0)
1118	+	{
1119	+
1120	+
1121	+	if (update_arg( (void *)&(args_info->length_arg),
1122	+	&(args_info->length_orig), &(args_info->length_given),
1123	+	&(local_args_info.length_given), optarg, 0, 0, ARG_DOUBLE,
1124	+	check_ambiguity, override, 0, 0,
1125	+	"length", '-',
1126	+	additional_error))
1127	+	goto failure;
1128	+
1129	+	}
1130	+	/* maximum length (Defaults to 1/2 smallest length of first frame).  */
1131	+	else if (strcmp (long_options[option_index].name, "zlength") == 0)
1132	+	{
1133	+
1134	+
1135	+	if (update_arg( (void *)&(args_info->zlength_arg),
1136	+	&(args_info->zlength_orig), &(args_info->zlength_given),
1137	+	&(local_args_info.zlength_given), optarg, 0, 0, ARG_DOUBLE,
1138	+	check_ambiguity, override, 0, 0,
1139	+	"zlength", '-',
1140	+	additional_error))
1141	+	goto failure;
1142	+
1143	+	}
1144	+	/* select the first stuntdouble set.  */
1145	+	else if (strcmp (long_options[option_index].name, "sele1") == 0)
1146	+	{
1147	+
1148	+
1149	+	if (update_arg( (void *)&(args_info->sele1_arg),
1150	+	&(args_info->sele1_orig), &(args_info->sele1_given),
1151	+	&(local_args_info.sele1_given), optarg, 0, 0, ARG_STRING,
1152	+	check_ambiguity, override, 0, 0,
1153	+	"sele1", '-',
1154	+	additional_error))
1155	+	goto failure;
1156	+
1157	+	}
1158		/* select the second stuntdouble set.  */
1159		else if (strcmp (long_options[option_index].name, "sele2") == 0)
1160		{
262	–	if (args_info->sele2_given)
263	–	{
264	–	fprintf (stderr, "%s: `--sele2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
265	–	clear_args ();
266	–	exit (EXIT_FAILURE);
267	–	}
268	–	args_info->sele2_given = 1;
269	–	args_info->sele2_arg = gengetopt_strdup (optarg);
270	–	break;
271	–	}
1161
1162	+
1163	+	if (update_arg( (void *)&(args_info->sele2_arg),
1164	+	&(args_info->sele2_orig), &(args_info->sele2_given),
1165	+	&(local_args_info.sele2_given), optarg, 0, 0, ARG_STRING,
1166	+	check_ambiguity, override, 0, 0,
1167	+	"sele2", '-',
1168	+	additional_error))
1169	+	goto failure;
1170	+
1171	+	}
1172		/* select the third stuntdouble set.  */
1173		else if (strcmp (long_options[option_index].name, "sele3") == 0)
1174		{
276	–	if (args_info->sele3_given)
277	–	{
278	–	fprintf (stderr, "%s: `--sele3' option given more than once\n", CMDLINE_PARSER_PACKAGE);
279	–	clear_args ();
280	–	exit (EXIT_FAILURE);
281	–	}
282	–	args_info->sele3_given = 1;
283	–	args_info->sele3_arg = gengetopt_strdup (optarg);
284	–	break;
285	–	}
1175
1176	+
1177	+	if (update_arg( (void *)&(args_info->sele3_arg),
1178	+	&(args_info->sele3_orig), &(args_info->sele3_given),
1179	+	&(local_args_info.sele3_given), optarg, 0, 0, ARG_STRING,
1180	+	check_ambiguity, override, 0, 0,
1181	+	"sele3", '-',
1182	+	additional_error))
1183	+	goto failure;
1184	+
1185	+	}
1186		/* select reference (use and only use with --gxyz).  */
1187		else if (strcmp (long_options[option_index].name, "refsele") == 0)
1188		{
1189	<	if (args_info->refsele_given)
1190	<	{
1191	<	fprintf (stderr, "%s: `--refsele' option given more than once\n", CMDLINE_PARSER_PACKAGE);
1192	<	clear_args ();
1193	<	exit (EXIT_FAILURE);
1194	<	}
1195	<	args_info->refsele_given = 1;
1196	<	args_info->refsele_arg = gengetopt_strdup (optarg);
1197	<	break;
1189	>
1190	>
1191	>	if (update_arg( (void *)&(args_info->refsele_arg),
1192	>	&(args_info->refsele_orig), &(args_info->refsele_given),
1193	>	&(local_args_info.refsele_given), optarg, 0, 0, ARG_STRING,
1194	>	check_ambiguity, override, 0, 0,
1195	>	"refsele", '-',
1196	>	additional_error))
1197	>	goto failure;
1198	>
1199		}
1200	+	/* select stunt doubles for center-of-mass reference point.  */
1201	+	else if (strcmp (long_options[option_index].name, "comsele") == 0)
1202	+	{
1203
1204	+
1205	+	if (update_arg( (void *)&(args_info->comsele_arg),
1206	+	&(args_info->comsele_orig), &(args_info->comsele_given),
1207	+	&(local_args_info.comsele_given), optarg, 0, 0, ARG_STRING,
1208	+	check_ambiguity, override, 0, 0,
1209	+	"comsele", '-',
1210	+	additional_error))
1211	+	goto failure;
1212	+
1213	+	}
1214		/* molecule name.  */
1215		else if (strcmp (long_options[option_index].name, "molname") == 0)
1216		{
304	–	if (args_info->molname_given)
305	–	{
306	–	fprintf (stderr, "%s: `--molname' option given more than once\n", CMDLINE_PARSER_PACKAGE);
307	–	clear_args ();
308	–	exit (EXIT_FAILURE);
309	–	}
310	–	args_info->molname_given = 1;
311	–	args_info->molname_arg = gengetopt_strdup (optarg);
312	–	break;
313	–	}
1217
1218	<	/* begin interanl index.  */
1218	>
1219	>	if (update_arg( (void *)&(args_info->molname_arg),
1220	>	&(args_info->molname_orig), &(args_info->molname_given),
1221	>	&(local_args_info.molname_given), optarg, 0, 0, ARG_STRING,
1222	>	check_ambiguity, override, 0, 0,
1223	>	"molname", '-',
1224	>	additional_error))
1225	>	goto failure;
1226	>
1227	>	}
1228	>	/* begin internal index.  */
1229		else if (strcmp (long_options[option_index].name, "begin") == 0)
1230		{
318	–	if (args_info->begin_given)
319	–	{
320	–	fprintf (stderr, "%s: `--begin' option given more than once\n", CMDLINE_PARSER_PACKAGE);
321	–	clear_args ();
322	–	exit (EXIT_FAILURE);
323	–	}
324	–	args_info->begin_given = 1;
325	–	args_info->begin_arg = strtol (optarg,&stop_char,0);
326	–	break;
327	–	}
1231
1232	+
1233	+	if (update_arg( (void *)&(args_info->begin_arg),
1234	+	&(args_info->begin_orig), &(args_info->begin_given),
1235	+	&(local_args_info.begin_given), optarg, 0, 0, ARG_INT,
1236	+	check_ambiguity, override, 0, 0,
1237	+	"begin", '-',
1238	+	additional_error))
1239	+	goto failure;
1240	+
1241	+	}
1242		/* end internal index.  */
1243		else if (strcmp (long_options[option_index].name, "end") == 0)
1244		{
332	–	if (args_info->end_given)
333	–	{
334	–	fprintf (stderr, "%s: `--end' option given more than once\n", CMDLINE_PARSER_PACKAGE);
335	–	clear_args ();
336	–	exit (EXIT_FAILURE);
337	–	}
338	–	args_info->end_given = 1;
339	–	args_info->end_arg = strtol (optarg,&stop_char,0);
340	–	break;
341	–	}
1245
1246	<	/* g(r).  */
1247	<	else if (strcmp (long_options[option_index].name, "gofr") == 0)
1246	>
1247	>	if (update_arg( (void *)&(args_info->end_arg),
1248	>	&(args_info->end_orig), &(args_info->end_given),
1249	>	&(local_args_info.end_given), optarg, 0, 0, ARG_INT,
1250	>	check_ambiguity, override, 0, 0,
1251	>	"end", '-',
1252	>	additional_error))
1253	>	goto failure;
1254	>
1255	>	}
1256	>	/* nanoparticle radius.  */
1257	>	else if (strcmp (long_options[option_index].name, "radius") == 0)
1258		{
346	–	if (args_info->gofr_given)
347	–	{
348	–	fprintf (stderr, "%s: `--gofr' option given more than once\n", CMDLINE_PARSER_PACKAGE);
349	–	clear_args ();
350	–	exit (EXIT_FAILURE);
351	–	}
352	–	args_info->gofr_given = 1; staticProps_group_counter += 1;
1259
1260	<	break;
1260	>
1261	>	if (update_arg( (void *)&(args_info->radius_arg),
1262	>	&(args_info->radius_orig), &(args_info->radius_given),
1263	>	&(local_args_info.radius_given), optarg, 0, 0, ARG_DOUBLE,
1264	>	check_ambiguity, override, 0, 0,
1265	>	"radius", '-',
1266	>	additional_error))
1267	>	goto failure;
1268	>
1269		}
1270	+	/* bond order parameter (--rcut must be specified).  */
1271	+	else if (strcmp (long_options[option_index].name, "bo") == 0)
1272	+	{
1273
1274	+	if (args_info->staticProps_group_counter && override)
1275	+	reset_group_staticProps (args_info);
1276	+	args_info->staticProps_group_counter += 1;
1277	+
1278	+	if (update_arg( 0 ,
1279	+	0 , &(args_info->bo_given),
1280	+	&(local_args_info.bo_given), optarg, 0, 0, ARG_NO,
1281	+	check_ambiguity, override, 0, 0,
1282	+	"bo", '-',
1283	+	additional_error))
1284	+	goto failure;
1285	+
1286	+	}
1287	+	/* bond order parameter as a function of radius (--rcut must be specified).  */
1288	+	else if (strcmp (long_options[option_index].name, "bor") == 0)
1289	+	{
1290	+
1291	+	if (args_info->staticProps_group_counter && override)
1292	+	reset_group_staticProps (args_info);
1293	+	args_info->staticProps_group_counter += 1;
1294	+
1295	+	if (update_arg( 0 ,
1296	+	0 , &(args_info->bor_given),
1297	+	&(local_args_info.bor_given), optarg, 0, 0, ARG_NO,
1298	+	check_ambiguity, override, 0, 0,
1299	+	"bor", '-',
1300	+	additional_error))
1301	+	goto failure;
1302	+
1303	+	}
1304	+	/* N(theta) bond angle density within (--rcut must be specified).  */
1305	+	else if (strcmp (long_options[option_index].name, "bad") == 0)
1306	+	{
1307	+
1308	+	if (args_info->staticProps_group_counter && override)
1309	+	reset_group_staticProps (args_info);
1310	+	args_info->staticProps_group_counter += 1;
1311	+
1312	+	if (update_arg( 0 ,
1313	+	0 , &(args_info->bad_given),
1314	+	&(local_args_info.bad_given), optarg, 0, 0, ARG_NO,
1315	+	check_ambiguity, override, 0, 0,
1316	+	"bad", '-',
1317	+	additional_error))
1318	+	goto failure;
1319	+
1320	+	}
1321	+	/* count of molecules matching selection criteria (and associated statistics).  */
1322	+	else if (strcmp (long_options[option_index].name, "count") == 0)
1323	+	{
1324	+
1325	+	if (args_info->staticProps_group_counter && override)
1326	+	reset_group_staticProps (args_info);
1327	+	args_info->staticProps_group_counter += 1;
1328	+
1329	+	if (update_arg( 0 ,
1330	+	0 , &(args_info->count_given),
1331	+	&(local_args_info.count_given), optarg, 0, 0, ARG_NO,
1332	+	check_ambiguity, override, 0, 0,
1333	+	"count", '-',
1334	+	additional_error))
1335	+	goto failure;
1336	+
1337	+	}
1338	+	/* g(z).  */
1339	+	else if (strcmp (long_options[option_index].name, "gofz") == 0)
1340	+	{
1341	+
1342	+	if (args_info->staticProps_group_counter && override)
1343	+	reset_group_staticProps (args_info);
1344	+	args_info->staticProps_group_counter += 1;
1345	+
1346	+	if (update_arg( 0 ,
1347	+	0 , &(args_info->gofz_given),
1348	+	&(local_args_info.gofz_given), optarg, 0, 0, ARG_NO,
1349	+	check_ambiguity, override, 0, 0,
1350	+	"gofz", '-',
1351	+	additional_error))
1352	+	goto failure;
1353	+
1354	+	}
1355		/* g(r, cos(theta)).  */
1356		else if (strcmp (long_options[option_index].name, "r_theta") == 0)
1357		{
360	–	if (args_info->r_theta_given)
361	–	{
362	–	fprintf (stderr, "%s: `--r_theta' option given more than once\n", CMDLINE_PARSER_PACKAGE);
363	–	clear_args ();
364	–	exit (EXIT_FAILURE);
365	–	}
366	–	args_info->r_theta_given = 1; staticProps_group_counter += 1;
1358
1359	<	break;
1360	<	}
1359	>	if (args_info->staticProps_group_counter && override)
1360	>	reset_group_staticProps (args_info);
1361	>	args_info->staticProps_group_counter += 1;
1362
1363	+	if (update_arg( 0 ,
1364	+	0 , &(args_info->r_theta_given),
1365	+	&(local_args_info.r_theta_given), optarg, 0, 0, ARG_NO,
1366	+	check_ambiguity, override, 0, 0,
1367	+	"r_theta", '-',
1368	+	additional_error))
1369	+	goto failure;
1370	+
1371	+	}
1372		/* g(r, cos(omega)).  */
1373		else if (strcmp (long_options[option_index].name, "r_omega") == 0)
1374		{
374	–	if (args_info->r_omega_given)
375	–	{
376	–	fprintf (stderr, "%s: `--r_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
377	–	clear_args ();
378	–	exit (EXIT_FAILURE);
379	–	}
380	–	args_info->r_omega_given = 1; staticProps_group_counter += 1;
1375
1376	<	break;
1376	>	if (args_info->staticProps_group_counter && override)
1377	>	reset_group_staticProps (args_info);
1378	>	args_info->staticProps_group_counter += 1;
1379	>
1380	>	if (update_arg( 0 ,
1381	>	0 , &(args_info->r_omega_given),
1382	>	&(local_args_info.r_omega_given), optarg, 0, 0, ARG_NO,
1383	>	check_ambiguity, override, 0, 0,
1384	>	"r_omega", '-',
1385	>	additional_error))
1386	>	goto failure;
1387	>
1388		}
1389	+	/* g(r, z).  */
1390	+	else if (strcmp (long_options[option_index].name, "r_z") == 0)
1391	+	{
1392
1393	+	if (args_info->staticProps_group_counter && override)
1394	+	reset_group_staticProps (args_info);
1395	+	args_info->staticProps_group_counter += 1;
1396	+
1397	+	if (update_arg( 0 ,
1398	+	0 , &(args_info->r_z_given),
1399	+	&(local_args_info.r_z_given), optarg, 0, 0, ARG_NO,
1400	+	check_ambiguity, override, 0, 0,
1401	+	"r_z", '-',
1402	+	additional_error))
1403	+	goto failure;
1404	+
1405	+	}
1406		/* g(cos(theta), cos(omega)).  */
1407		else if (strcmp (long_options[option_index].name, "theta_omega") == 0)
1408		{
388	–	if (args_info->theta_omega_given)
389	–	{
390	–	fprintf (stderr, "%s: `--theta_omega' option given more than once\n", CMDLINE_PARSER_PACKAGE);
391	–	clear_args ();
392	–	exit (EXIT_FAILURE);
393	–	}
394	–	args_info->theta_omega_given = 1; staticProps_group_counter += 1;
1409
1410	<	break;
1411	<	}
1410	>	if (args_info->staticProps_group_counter && override)
1411	>	reset_group_staticProps (args_info);
1412	>	args_info->staticProps_group_counter += 1;
1413
1414	+	if (update_arg( 0 ,
1415	+	0 , &(args_info->theta_omega_given),
1416	+	&(local_args_info.theta_omega_given), optarg, 0, 0, ARG_NO,
1417	+	check_ambiguity, override, 0, 0,
1418	+	"theta_omega", '-',
1419	+	additional_error))
1420	+	goto failure;
1421	+
1422	+	}
1423		/* g(x, y, z).  */
1424		else if (strcmp (long_options[option_index].name, "gxyz") == 0)
1425		{
402	–	if (args_info->gxyz_given)
403	–	{
404	–	fprintf (stderr, "%s: `--gxyz' option given more than once\n", CMDLINE_PARSER_PACKAGE);
405	–	clear_args ();
406	–	exit (EXIT_FAILURE);
407	–	}
408	–	args_info->gxyz_given = 1; staticProps_group_counter += 1;
1426
1427	<	break;
1428	<	}
1427	>	if (args_info->staticProps_group_counter && override)
1428	>	reset_group_staticProps (args_info);
1429	>	args_info->staticProps_group_counter += 1;
1430
1431	<	/* p2 order parameter (--sele1 and --sele2 must be specified).  */
1432	<	else if (strcmp (long_options[option_index].name, "p2") == 0)
1431	>	if (update_arg( 0 ,
1432	>	0 , &(args_info->gxyz_given),
1433	>	&(local_args_info.gxyz_given), optarg, 0, 0, ARG_NO,
1434	>	check_ambiguity, override, 0, 0,
1435	>	"gxyz", '-',
1436	>	additional_error))
1437	>	goto failure;
1438	>
1439	>	}
1440	>	/* 2D g(r) (Slab width --dz must be specified).  */
1441	>	else if (strcmp (long_options[option_index].name, "twodgofr") == 0)
1442		{
416	–	if (args_info->p2_given)
417	–	{
418	–	fprintf (stderr, "%s: `--p2' option given more than once\n", CMDLINE_PARSER_PACKAGE);
419	–	clear_args ();
420	–	exit (EXIT_FAILURE);
421	–	}
422	–	args_info->p2_given = 1; staticProps_group_counter += 1;
1443
1444	<	break;
1444	>	if (args_info->staticProps_group_counter && override)
1445	>	reset_group_staticProps (args_info);
1446	>	args_info->staticProps_group_counter += 1;
1447	>
1448	>	if (update_arg( 0 ,
1449	>	0 , &(args_info->twodgofr_given),
1450	>	&(local_args_info.twodgofr_given), optarg, 0, 0, ARG_NO,
1451	>	check_ambiguity, override, 0, 0,
1452	>	"twodgofr", '-',
1453	>	additional_error))
1454	>	goto failure;
1455	>
1456		}
1457	+	/* rp2 order parameter (--sele1 and --sele2 must be specified).  */
1458	+	else if (strcmp (long_options[option_index].name, "rp2") == 0)
1459	+	{
1460
1461	<	/* scd order parameter(either --sele1, --sele2, --sele3 are specified or --molname, --begin, --end are specified).  */
1462	<	else if (strcmp (long_options[option_index].name, "scd") == 0)
1461	>	if (args_info->staticProps_group_counter && override)
1462	>	reset_group_staticProps (args_info);
1463	>	args_info->staticProps_group_counter += 1;
1464	>
1465	>	if (update_arg( 0 ,
1466	>	0 , &(args_info->rp2_given),
1467	>	&(local_args_info.rp2_given), optarg, 0, 0, ARG_NO,
1468	>	check_ambiguity, override, 0, 0,
1469	>	"rp2", '-',
1470	>	additional_error))
1471	>	goto failure;
1472	>
1473	>	}
1474	>	/* slab density.  */
1475	>	else if (strcmp (long_options[option_index].name, "slab_density") == 0)
1476		{
430	–	if (args_info->scd_given)
431	–	{
432	–	fprintf (stderr, "%s: `--scd' option given more than once\n", CMDLINE_PARSER_PACKAGE);
433	–	clear_args ();
434	–	exit (EXIT_FAILURE);
435	–	}
436	–	args_info->scd_given = 1; staticProps_group_counter += 1;
1477
1478	<	break;
1478	>	if (args_info->staticProps_group_counter && override)
1479	>	reset_group_staticProps (args_info);
1480	>	args_info->staticProps_group_counter += 1;
1481	>
1482	>	if (update_arg( 0 ,
1483	>	0 , &(args_info->slab_density_given),
1484	>	&(local_args_info.slab_density_given), optarg, 0, 0, ARG_NO,
1485	>	check_ambiguity, override, 0, 0,
1486	>	"slab_density", '-',
1487	>	additional_error))
1488	>	goto failure;
1489	>
1490		}
1491	+	/* p(cos(theta)).  */
1492	+	else if (strcmp (long_options[option_index].name, "p_angle") == 0)
1493	+	{
1494
1495	<
1495	>	if (args_info->staticProps_group_counter && override)
1496	>	reset_group_staticProps (args_info);
1497	>	args_info->staticProps_group_counter += 1;
1498	>
1499	>	if (update_arg( 0 ,
1500	>	0 , &(args_info->p_angle_given),
1501	>	&(local_args_info.p_angle_given), optarg, 0, 0, ARG_NO,
1502	>	check_ambiguity, override, 0, 0,
1503	>	"p_angle", '-',
1504	>	additional_error))
1505	>	goto failure;
1506	>
1507	>	}
1508	>	/* hxy.  */
1509	>	else if (strcmp (long_options[option_index].name, "hxy") == 0)
1510	>	{
1511	>
1512	>	if (args_info->staticProps_group_counter && override)
1513	>	reset_group_staticProps (args_info);
1514	>	args_info->staticProps_group_counter += 1;
1515	>
1516	>	if (update_arg( 0 ,
1517	>	0 , &(args_info->hxy_given),
1518	>	&(local_args_info.hxy_given), optarg, 0, 0, ARG_NO,
1519	>	check_ambiguity, override, 0, 0,
1520	>	"hxy", '-',
1521	>	additional_error))
1522	>	goto failure;
1523	>
1524	>	}
1525	>	/* rho of R.  */
1526	>	else if (strcmp (long_options[option_index].name, "rho_r") == 0)
1527	>	{
1528	>
1529	>	if (args_info->staticProps_group_counter && override)
1530	>	reset_group_staticProps (args_info);
1531	>	args_info->staticProps_group_counter += 1;
1532	>
1533	>	if (update_arg( 0 ,
1534	>	0 , &(args_info->rho_r_given),
1535	>	&(local_args_info.rho_r_given), optarg, 0, 0, ARG_NO,
1536	>	check_ambiguity, override, 0, 0,
1537	>	"rho_r", '-',
1538	>	additional_error))
1539	>	goto failure;
1540	>
1541	>	}
1542	>	/* angle of R.  */
1543	>	else if (strcmp (long_options[option_index].name, "angle_r") == 0)
1544	>	{
1545	>
1546	>	if (args_info->staticProps_group_counter && override)
1547	>	reset_group_staticProps (args_info);
1548	>	args_info->staticProps_group_counter += 1;
1549	>
1550	>	if (update_arg( 0 ,
1551	>	0 , &(args_info->angle_r_given),
1552	>	&(local_args_info.angle_r_given), optarg, 0, 0, ARG_NO,
1553	>	check_ambiguity, override, 0, 0,
1554	>	"angle_r", '-',
1555	>	additional_error))
1556	>	goto failure;
1557	>
1558	>	}
1559	>	/* hull volume of nanoparticle.  */
1560	>	else if (strcmp (long_options[option_index].name, "hullvol") == 0)
1561	>	{
1562	>
1563	>	if (args_info->staticProps_group_counter && override)
1564	>	reset_group_staticProps (args_info);
1565	>	args_info->staticProps_group_counter += 1;
1566	>
1567	>	if (update_arg( 0 ,
1568	>	0 , &(args_info->hullvol_given),
1569	>	&(local_args_info.hullvol_given), optarg, 0, 0, ARG_NO,
1570	>	check_ambiguity, override, 0, 0,
1571	>	"hullvol", '-',
1572	>	additional_error))
1573	>	goto failure;
1574	>
1575	>	}
1576	>	/* length of nanorod.  */
1577	>	else if (strcmp (long_options[option_index].name, "rodlength") == 0)
1578	>	{
1579	>
1580	>	if (args_info->staticProps_group_counter && override)
1581	>	reset_group_staticProps (args_info);
1582	>	args_info->staticProps_group_counter += 1;
1583	>
1584	>	if (update_arg( 0 ,
1585	>	0 , &(args_info->rodlength_given),
1586	>	&(local_args_info.rodlength_given), optarg, 0, 0, ARG_NO,
1587	>	check_ambiguity, override, 0, 0,
1588	>	"rodlength", '-',
1589	>	additional_error))
1590	>	goto failure;
1591	>
1592	>	}
1593	>	/* tetrahedrality order parameter by zbin(--sele1 must be specified).  */
1594	>	else if (strcmp (long_options[option_index].name, "tet_param_z") == 0)
1595	>	{
1596	>
1597	>	if (args_info->staticProps_group_counter && override)
1598	>	reset_group_staticProps (args_info);
1599	>	args_info->staticProps_group_counter += 1;
1600	>
1601	>	if (update_arg( 0 ,
1602	>	0 , &(args_info->tet_param_z_given),
1603	>	&(local_args_info.tet_param_z_given), optarg, 0, 0, ARG_NO,
1604	>	check_ambiguity, override, 0, 0,
1605	>	"tet_param_z", '-',
1606	>	additional_error))
1607	>	goto failure;
1608	>
1609	>	}
1610	>
1611	>	break;
1612		case '?':       /* Invalid option.  */
1613		/* `getopt_long' already printed an error message.  */
1614	<	exit (EXIT_FAILURE);
1614	>	goto failure;
1615
1616		default:        /* bug: option not considered.  */
1617	<	fprintf (stderr, "%s: option unknown: %c\n", CMDLINE_PARSER_PACKAGE, c);
1617	>	fprintf (stderr, "%s: option unknown: %c%s\n", CMDLINE_PARSER_PACKAGE, c, (additional_error ? additional_error : ""));
1618		abort ();
1619		} /* switch */
1620		} /* while */
1621
1622	<	if ( staticProps_group_counter != 1)
1622	>	if (args_info->staticProps_group_counter > 1)
1623		{
1624	<	fprintf (stderr, "%s: %d options of group staticProps were given. One is required\n", CMDLINE_PARSER_PACKAGE, staticProps_group_counter);
1625	<	missing_required_options = 1;
1624	>	fprintf (stderr, "%s: %d options of group staticProps were given. One is required%s.\n", argv[0], args_info->staticProps_group_counter, (additional_error ? additional_error : ""));
1625	>	error = 1;
1626		}
1627
1628
1629	<	if (! args_info->input_given)
1629	>
1630	>	if (check_required)
1631		{
1632	<	fprintf (stderr, "%s: '--input' ('-i') option required\n", CMDLINE_PARSER_PACKAGE);
462	<	missing_required_options = 1;
1632	>	error += cmdline_parser_required2 (args_info, argv[0], additional_error);
1633		}
464	–	if ( missing_required_options )
465	–	exit (EXIT_FAILURE);
1634
1635	+	cmdline_parser_release (&local_args_info);
1636	+
1637	+	if ( error )
1638	+	return (EXIT_FAILURE);
1639	+
1640	+	if (optind < argc)
1641	+	{
1642	+	int i = 0 ;
1643	+	int found_prog_name = 0;
1644	+	/* whether program name, i.e., argv[0], is in the remaining args
1645	+	(this may happen with some implementations of getopt,
1646	+	but surely not with the one included by gengetopt) */
1647	+
1648	+	i = optind;
1649	+	while (i < argc)
1650	+	if (argv[i++] == argv[0]) {
1651	+	found_prog_name = 1;
1652	+	break;
1653	+	}
1654	+	i = 0;
1655	+
1656	+	args_info->inputs_num = argc - optind - found_prog_name;
1657	+	args_info->inputs =
1658	+	(char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
1659	+	while (optind < argc)
1660	+	if (argv[optind++] != argv[0])
1661	+	args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
1662	+	}
1663	+
1664		return 0;
1665	+
1666	+	failure:
1667	+
1668	+	cmdline_parser_release (&local_args_info);
1669	+	return (EXIT_FAILURE);
1670		}

Comparing:
trunk/src/applications/staticProps/StaticPropsCmd.c (property svn:keywords), Revision 544 by tim, Fri May 27 04:41:34 2005 UTC vs.
trunk/src/applications/staticProps/StaticPropsCmd.cpp (property svn:keywords), Revision 1795 by gezelter, Fri Sep 7 18:13:55 2012 UTC

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